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.\" ========================================================================
.\"
.IX Title "MAGE::Array::Fiducial 3pm"
.TH MAGE::Array::Fiducial 3pm "2018-10-24" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::MAGE::Array::Fiducial \- Class for the MAGE\-OM API
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::MAGE::Array::Fiducial
\&
\&  # creating an empty instance
\&  my $fiducial = Bio::MAGE::Array::Fiducial\->new();
\&
\&  # creating an instance with existing data
\&  my $fiducial = Bio::MAGE::Array::Fiducial\->new(
\&        position=>$position_ref,
\&        auditTrail=>\e@audit_list,
\&        propertySets=>\e@namevaluetype_list,
\&        distanceUnit=>$distanceunit_ref,
\&        descriptions=>\e@description_list,
\&        security=>$security_ref,
\&        fiducialType=>$ontologyentry_ref,
\&  );
\&
\&
\&
\&  # \*(Aqposition\*(Aq association
\&  my $position_ref = $fiducial\->position(); # getter
\&  $fiducial\->position($position_ref); # setter
\&
\&  # \*(AqauditTrail\*(Aq association
\&  my $audit_array_ref = $fiducial\->auditTrail(); # getter
\&  $fiducial\->auditTrail(\e@audit_list); # setter
\&
\&  # \*(AqpropertySets\*(Aq association
\&  my $namevaluetype_array_ref = $fiducial\->propertySets(); # getter
\&  $fiducial\->propertySets(\e@namevaluetype_list); # setter
\&
\&  # \*(AqdistanceUnit\*(Aq association
\&  my $distanceunit_ref = $fiducial\->distanceUnit(); # getter
\&  $fiducial\->distanceUnit($distanceunit_ref); # setter
\&
\&  # \*(Aqdescriptions\*(Aq association
\&  my $description_array_ref = $fiducial\->descriptions(); # getter
\&  $fiducial\->descriptions(\e@description_list); # setter
\&
\&  # \*(Aqsecurity\*(Aq association
\&  my $security_ref = $fiducial\->security(); # getter
\&  $fiducial\->security($security_ref); # setter
\&
\&  # \*(AqfiducialType\*(Aq association
\&  my $ontologyentry_ref = $fiducial\->fiducialType(); # getter
\&  $fiducial\->fiducialType($ontologyentry_ref); # setter
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
From the MAGE-OM documentation for the \f(CW\*(C`Fiducial\*(C'\fR class:
.PP
A marking on the surface of the array that can be used to identify the array's origin, the coordinates of which are the fiducial's centroid.
.SH "INHERITANCE"
.IX Header "INHERITANCE"
Bio::MAGE::Array::Fiducial has the following superclasses:
.IP "\(bu" 4
Bio::MAGE::Describable
.SH "CLASS METHODS"
.IX Header "CLASS METHODS"
The following methods can all be called without first having an
instance of the class via the Bio::MAGE::Array::Fiducial\->\fImethodname()\fR syntax.
.IP "\fInew()\fR" 4
.IX Item "new()"
.PD 0
.IP "new(%args)" 4
.IX Item "new(%args)"
.PD
The object constructor \f(CW\*(C`new()\*(C'\fR accepts the following optional
named-value style arguments:
.RS 4
.IP "\(bu" 4
auditTrail
.Sp
Sets the value of the \f(CW\*(C`auditTrail\*(C'\fR association (this association was inherited from class \f(CW\*(C`Bio::MAGE::Describable\*(C'\fR).
.Sp
The value must be of type: array of \f(CW\*(C`Bio::MAGE::AuditAndSecurity::Audit\*(C'\fR.
.IP "\(bu" 4
position
.Sp
Sets the value of the \f(CW\*(C`position\*(C'\fR association
.Sp
The value must be of type: instance of \f(CW\*(C`Bio::MAGE::DesignElement::Position\*(C'\fR.
.IP "\(bu" 4
propertySets
.Sp
Sets the value of the \f(CW\*(C`propertySets\*(C'\fR association (this association was inherited from class \f(CW\*(C`Bio::MAGE::Extendable\*(C'\fR).
.Sp
The value must be of type: array of \f(CW\*(C`Bio::MAGE::NameValueType\*(C'\fR.
.IP "\(bu" 4
descriptions
.Sp
Sets the value of the \f(CW\*(C`descriptions\*(C'\fR association (this association was inherited from class \f(CW\*(C`Bio::MAGE::Describable\*(C'\fR).
.Sp
The value must be of type: array of \f(CW\*(C`Bio::MAGE::Description::Description\*(C'\fR.
.IP "\(bu" 4
distanceUnit
.Sp
Sets the value of the \f(CW\*(C`distanceUnit\*(C'\fR association
.Sp
The value must be of type: instance of \f(CW\*(C`Bio::MAGE::Measurement::DistanceUnit\*(C'\fR.
.IP "\(bu" 4
security
.Sp
Sets the value of the \f(CW\*(C`security\*(C'\fR association (this association was inherited from class \f(CW\*(C`Bio::MAGE::Describable\*(C'\fR).
.Sp
The value must be of type: instance of \f(CW\*(C`Bio::MAGE::AuditAndSecurity::Security\*(C'\fR.
.IP "\(bu" 4
fiducialType
.Sp
Sets the value of the \f(CW\*(C`fiducialType\*(C'\fR association
.Sp
The value must be of type: instance of \f(CW\*(C`Bio::MAGE::Description::OntologyEntry\*(C'\fR.
.RE
.RS 4
.RE
.ie n .IP "$obj = class\->new(%parameters)" 4
.el .IP "\f(CW$obj\fR = class\->new(%parameters)" 4
.IX Item "$obj = class->new(%parameters)"
The \f(CW\*(C`new()\*(C'\fR method is the class constructor.
.Sp
\&\fBParameters\fR: if given a list of name/value parameters the
corresponding slots, attributes, or associations will have their
initial values set by the constructor.
.Sp
\&\fBReturn value\fR: It returns a reference to an object of the class.
.Sp
\&\fBSide effects\fR: It invokes the \f(CW\*(C`initialize()\*(C'\fR method if it is defined
by the class.
.ie n .IP "@names = class\->\fIget_slot_names()\fR" 4
.el .IP "\f(CW@names\fR = class\->\fIget_slot_names()\fR" 4
.IX Item "@names = class->get_slot_names()"
The \f(CW\*(C`get_slot_names()\*(C'\fR method is used to retrieve the name of all
slots defined in a given class.
.Sp
\&\fB\s-1NOTE\s0\fR: the list of names does not include attribute or association
names.
.Sp
\&\fBReturn value\fR: A list of the names of all slots defined for this class.
.Sp
\&\fBSide effects\fR: none
.ie n .IP "@name_list = \fIget_attribute_names()\fR" 4
.el .IP "\f(CW@name_list\fR = \fIget_attribute_names()\fR" 4
.IX Item "@name_list = get_attribute_names()"
returns the list of attribute data members for this class.
.ie n .IP "@name_list = \fIget_association_names()\fR" 4
.el .IP "\f(CW@name_list\fR = \fIget_association_names()\fR" 4
.IX Item "@name_list = get_association_names()"
returns the list of association data members for this class.
.ie n .IP "@class_list = \fIget_superclasses()\fR" 4
.el .IP "\f(CW@class_list\fR = \fIget_superclasses()\fR" 4
.IX Item "@class_list = get_superclasses()"
returns the list of superclasses for this class.
.ie n .IP "@class_list = \fIget_subclasses()\fR" 4
.el .IP "\f(CW@class_list\fR = \fIget_subclasses()\fR" 4
.IX Item "@class_list = get_subclasses()"
returns the list of subclasses for this class.
.ie n .IP "$name = \fIclass_name()\fR" 4
.el .IP "\f(CW$name\fR = \fIclass_name()\fR" 4
.IX Item "$name = class_name()"
Returns the full class name for this class.
.ie n .IP "$package_name = \fIpackage_name()\fR" 4
.el .IP "\f(CW$package_name\fR = \fIpackage_name()\fR" 4
.IX Item "$package_name = package_name()"
Returns the base package name (i.e. no 'namespace::') of the package
that contains this class.
.ie n .IP "%assns = \fIassociations()\fR" 4
.el .IP "\f(CW%assns\fR = \fIassociations()\fR" 4
.IX Item "%assns = associations()"
returns the association meta-information in a hash where the keys are
the association names and the values are \f(CW\*(C`Association\*(C'\fR objects that
provide the meta-information for the association.
.SH "INSTANCE METHODS"
.IX Header "INSTANCE METHODS"
.ie n .IP "$obj_copy = $obj\->\fInew()\fR" 4
.el .IP "\f(CW$obj_copy\fR = \f(CW$obj\fR\->\fInew()\fR" 4
.IX Item "$obj_copy = $obj->new()"
When invoked with an existing object reference and not a class name,
the \f(CW\*(C`new()\*(C'\fR method acts as a copy constructor \- with the new object's
initial values set to be those of the existing object.
.Sp
\&\fBParameters\fR: No input parameters  are used in the copy  constructor,
the initial values are taken directly from the object to be copied.
.Sp
\&\fBReturn value\fR: It returns a reference to an object of the class.
.Sp
\&\fBSide effects\fR: It invokes the \f(CW\*(C`initialize()\*(C'\fR method if it is defined
by the class.
.ie n .IP "$obj\->set_slots(%parameters)" 4
.el .IP "\f(CW$obj\fR\->set_slots(%parameters)" 4
.IX Item "$obj->set_slots(%parameters)"
.PD 0
.ie n .IP "$obj\->set_slots(\e@name_list, \e@value_list)" 4
.el .IP "\f(CW$obj\fR\->set_slots(\e@name_list, \e@value_list)" 4
.IX Item "$obj->set_slots(@name_list, @value_list)"
.PD
The \f(CW\*(C`set_slots()\*(C'\fR method is used to set a number of slots at the same
time. It has two different invocation methods. The first takes a named
parameter list, and the second takes two array references.
.Sp
\&\fBReturn value\fR: none
.Sp
\&\fBSide effects\fR: will call \f(CW\*(C`croak()\*(C'\fR if a slot_name is used that the class
does not define.
.ie n .IP "@obj_list = $obj\->get_slots(@name_list)" 4
.el .IP "\f(CW@obj_list\fR = \f(CW$obj\fR\->get_slots(@name_list)" 4
.IX Item "@obj_list = $obj->get_slots(@name_list)"
The \f(CW\*(C`get_slots()\*(C'\fR method is used to get the values of a number of
slots at the same time.
.Sp
\&\fBReturn value\fR: a list of instance objects
.Sp
\&\fBSide effects\fR: none
.ie n .IP "$val = $obj\->set_slot($name,$val)" 4
.el .IP "\f(CW$val\fR = \f(CW$obj\fR\->set_slot($name,$val)" 4
.IX Item "$val = $obj->set_slot($name,$val)"
The \f(CW\*(C`set_slot()\*(C'\fR method sets the slot \f(CW$name\fR to the value \f(CW$val\fR
.Sp
\&\fBReturn value\fR: the new value of the slot, i.e. \f(CW$val\fR
.Sp
\&\fBSide effects\fR: none
.ie n .IP "$val = $obj\->get_slot($name)" 4
.el .IP "\f(CW$val\fR = \f(CW$obj\fR\->get_slot($name)" 4
.IX Item "$val = $obj->get_slot($name)"
The \f(CW\*(C`get_slot()\*(C'\fR method is used to get the values of a number of
slots at the same time.
.Sp
\&\fBReturn value\fR: a single slot value, or undef if the slot has not been
initialized.
.Sp
\&\fBSide effects\fR: none
.SS "\s-1ATTRIBUTES\s0"
.IX Subsection "ATTRIBUTES"
Attributes are simple data types that belong to a single instance of a
class. In the Perl implementation of the MAGE-OM classes, the
interface to attributes is implemented using separate setter and
getter methods for each attribute.
.PP
\&\f(CW\*(C`Bio::MAGE::Array::Fiducial\*(C'\fR has the following attribute accessor methods:
.SS "\s-1ASSOCIATIONS\s0"
.IX Subsection "ASSOCIATIONS"
Associations are references to other classes. Associations in MAGE-OM have a cardinality that determines the minimum and
maximum number of instances of the 'other' class that maybe included
in the association:
.IP "1." 4
There \fBmust\fR be exactly one item in the association, i.e. this is a
mandatory data field.
.IP "2." 4
0..1
.Sp
There \fBmay\fR be one item in the association, i.e. this is an optional
data field.
.IP "3." 4
1..N
.Sp
There \fBmust\fR be one or more items in the association, i.e. this is a
mandatory data field, with list cardinality.
.IP "4." 4
0..N
.Sp
There \fBmay\fR be one or more items in the association, i.e. this is an
optional data field, with list cardinality.
.PP
Bio::MAGE::Array::Fiducial has the following association accessor methods:
.IP "auditTrail" 4
.IX Item "auditTrail"
Methods for the \f(CW\*(C`auditTrail\*(C'\fR association.
.Sp
From the MAGE-OM documentation:
.Sp
A list of Audit instances that track changes to the instance of Describable.
.RS 4
.ie n .IP "$array_ref = $fiducial\->setAuditTrail($array_ref)" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$fiducial\fR\->setAuditTrail($array_ref)" 4
.IX Item "$array_ref = $fiducial->setAuditTrail($array_ref)"
The restricted setter method for the \f(CW\*(C`auditTrail\*(C'\fR association.
.Sp
Input parameters: the value to which the \f(CW\*(C`auditTrail\*(C'\fR association will be set : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::AuditAndSecurity::Audit\*(C'\fR
.Sp
Return value: the current value of the \f(CW\*(C`auditTrail\*(C'\fR association : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::AuditAndSecurity::Audit\*(C'\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or
if too many input parameters are specified, or if \f(CW$array_ref\fR is not a reference to an array class \f(CW\*(C`Bio::MAGE::AuditAndSecurity::Audit\*(C'\fR instances
.ie n .IP "$array_ref = $fiducial\->\fIgetAuditTrail()\fR" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$fiducial\fR\->\fIgetAuditTrail()\fR" 4
.IX Item "$array_ref = $fiducial->getAuditTrail()"
The restricted getter method for the \f(CW\*(C`auditTrail\*(C'\fR association.
.Sp
Input parameters: none
.Sp
Return value: the current value of the \f(CW\*(C`auditTrail\*(C'\fR association : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::AuditAndSecurity::Audit\*(C'\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if any input parameters are specified
.ie n .IP "$val = $fiducial\->addAuditTrail(@vals)" 4
.el .IP "\f(CW$val\fR = \f(CW$fiducial\fR\->addAuditTrail(@vals)" 4
.IX Item "$val = $fiducial->addAuditTrail(@vals)"
Because the auditTrail association has list cardinality, it may store more
than one value. This method adds the current list of objects in the auditTrail association.
.Sp
Input parameters: the list of values \f(CW@vals\fR to add to the auditTrail association. \fB\s-1NOTE\s0\fR: submitting a single value is permitted.
.Sp
Return value: the number of items stored in the slot \fBafter\fR adding \f(CW@vals\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or if any of the objects in \f(CW@vals\fR is not an instance of class \f(CW\*(C`Bio::MAGE::AuditAndSecurity::Audit\*(C'\fR
.RE
.RS 4
.RE
.IP "position" 4
.IX Item "position"
Methods for the \f(CW\*(C`position\*(C'\fR association.
.Sp
From the MAGE-OM documentation:
.Sp
The position, relative to the upper left corner, of the fiducial
.RS 4
.ie n .IP "$val = $fiducial\->setPosition($val)" 4
.el .IP "\f(CW$val\fR = \f(CW$fiducial\fR\->setPosition($val)" 4
.IX Item "$val = $fiducial->setPosition($val)"
The restricted setter method for the \f(CW\*(C`position\*(C'\fR association.
.Sp
Input parameters: the value to which the \f(CW\*(C`position\*(C'\fR association will be set : one of the accepted enumerated values.
.Sp
Return value: the current value of the \f(CW\*(C`position\*(C'\fR association : one of the accepted enumerated values.
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or
if too many input parameters are specified, or if \f(CW$val\fR is not an instance of class \f(CW\*(C`Bio::MAGE::DesignElement::Position\*(C'\fR
.ie n .IP "$val = $fiducial\->\fIgetPosition()\fR" 4
.el .IP "\f(CW$val\fR = \f(CW$fiducial\fR\->\fIgetPosition()\fR" 4
.IX Item "$val = $fiducial->getPosition()"
The restricted getter method for the \f(CW\*(C`position\*(C'\fR association.
.Sp
Input parameters: none
.Sp
Return value: the current value of the \f(CW\*(C`position\*(C'\fR association : an instance of type \f(CW\*(C`Bio::MAGE::DesignElement::Position\*(C'\fR.
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if any input parameters are specified
.RE
.RS 4
.RE
.IP "propertySets" 4
.IX Item "propertySets"
Methods for the \f(CW\*(C`propertySets\*(C'\fR association.
.Sp
From the MAGE-OM documentation:
.Sp
Allows specification of name/value pairs.  Meant to primarily help in-house, pipeline processing of instances by providing a place for values that aren't part of the specification proper.
.RS 4
.ie n .IP "$array_ref = $fiducial\->setPropertySets($array_ref)" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$fiducial\fR\->setPropertySets($array_ref)" 4
.IX Item "$array_ref = $fiducial->setPropertySets($array_ref)"
The restricted setter method for the \f(CW\*(C`propertySets\*(C'\fR association.
.Sp
Input parameters: the value to which the \f(CW\*(C`propertySets\*(C'\fR association will be set : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::NameValueType\*(C'\fR
.Sp
Return value: the current value of the \f(CW\*(C`propertySets\*(C'\fR association : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::NameValueType\*(C'\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or
if too many input parameters are specified, or if \f(CW$array_ref\fR is not a reference to an array class \f(CW\*(C`Bio::MAGE::NameValueType\*(C'\fR instances
.ie n .IP "$array_ref = $fiducial\->\fIgetPropertySets()\fR" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$fiducial\fR\->\fIgetPropertySets()\fR" 4
.IX Item "$array_ref = $fiducial->getPropertySets()"
The restricted getter method for the \f(CW\*(C`propertySets\*(C'\fR association.
.Sp
Input parameters: none
.Sp
Return value: the current value of the \f(CW\*(C`propertySets\*(C'\fR association : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::NameValueType\*(C'\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if any input parameters are specified
.ie n .IP "$val = $fiducial\->addPropertySets(@vals)" 4
.el .IP "\f(CW$val\fR = \f(CW$fiducial\fR\->addPropertySets(@vals)" 4
.IX Item "$val = $fiducial->addPropertySets(@vals)"
Because the propertySets association has list cardinality, it may store more
than one value. This method adds the current list of objects in the propertySets association.
.Sp
Input parameters: the list of values \f(CW@vals\fR to add to the propertySets association. \fB\s-1NOTE\s0\fR: submitting a single value is permitted.
.Sp
Return value: the number of items stored in the slot \fBafter\fR adding \f(CW@vals\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or if any of the objects in \f(CW@vals\fR is not an instance of class \f(CW\*(C`Bio::MAGE::NameValueType\*(C'\fR
.RE
.RS 4
.RE
.IP "descriptions" 4
.IX Item "descriptions"
Methods for the \f(CW\*(C`descriptions\*(C'\fR association.
.Sp
From the MAGE-OM documentation:
.Sp
Free hand text descriptions.  Makes available the associations of Description to an instance of Describable.
.RS 4
.ie n .IP "$array_ref = $fiducial\->setDescriptions($array_ref)" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$fiducial\fR\->setDescriptions($array_ref)" 4
.IX Item "$array_ref = $fiducial->setDescriptions($array_ref)"
The restricted setter method for the \f(CW\*(C`descriptions\*(C'\fR association.
.Sp
Input parameters: the value to which the \f(CW\*(C`descriptions\*(C'\fR association will be set : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::Description::Description\*(C'\fR
.Sp
Return value: the current value of the \f(CW\*(C`descriptions\*(C'\fR association : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::Description::Description\*(C'\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or
if too many input parameters are specified, or if \f(CW$array_ref\fR is not a reference to an array class \f(CW\*(C`Bio::MAGE::Description::Description\*(C'\fR instances
.ie n .IP "$array_ref = $fiducial\->\fIgetDescriptions()\fR" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$fiducial\fR\->\fIgetDescriptions()\fR" 4
.IX Item "$array_ref = $fiducial->getDescriptions()"
The restricted getter method for the \f(CW\*(C`descriptions\*(C'\fR association.
.Sp
Input parameters: none
.Sp
Return value: the current value of the \f(CW\*(C`descriptions\*(C'\fR association : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::Description::Description\*(C'\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if any input parameters are specified
.ie n .IP "$val = $fiducial\->addDescriptions(@vals)" 4
.el .IP "\f(CW$val\fR = \f(CW$fiducial\fR\->addDescriptions(@vals)" 4
.IX Item "$val = $fiducial->addDescriptions(@vals)"
Because the descriptions association has list cardinality, it may store more
than one value. This method adds the current list of objects in the descriptions association.
.Sp
Input parameters: the list of values \f(CW@vals\fR to add to the descriptions association. \fB\s-1NOTE\s0\fR: submitting a single value is permitted.
.Sp
Return value: the number of items stored in the slot \fBafter\fR adding \f(CW@vals\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or if any of the objects in \f(CW@vals\fR is not an instance of class \f(CW\*(C`Bio::MAGE::Description::Description\*(C'\fR
.RE
.RS 4
.RE
.IP "distanceUnit" 4
.IX Item "distanceUnit"
Methods for the \f(CW\*(C`distanceUnit\*(C'\fR association.
.Sp
From the MAGE-OM documentation:
.Sp
The units the fiducial is measured in.
.RS 4
.ie n .IP "$val = $fiducial\->setDistanceUnit($val)" 4
.el .IP "\f(CW$val\fR = \f(CW$fiducial\fR\->setDistanceUnit($val)" 4
.IX Item "$val = $fiducial->setDistanceUnit($val)"
The restricted setter method for the \f(CW\*(C`distanceUnit\*(C'\fR association.
.Sp
Input parameters: the value to which the \f(CW\*(C`distanceUnit\*(C'\fR association will be set : one of the accepted enumerated values.
.Sp
Return value: the current value of the \f(CW\*(C`distanceUnit\*(C'\fR association : one of the accepted enumerated values.
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or
if too many input parameters are specified, or if \f(CW$val\fR is not an instance of class \f(CW\*(C`Bio::MAGE::Measurement::DistanceUnit\*(C'\fR
.ie n .IP "$val = $fiducial\->\fIgetDistanceUnit()\fR" 4
.el .IP "\f(CW$val\fR = \f(CW$fiducial\fR\->\fIgetDistanceUnit()\fR" 4
.IX Item "$val = $fiducial->getDistanceUnit()"
The restricted getter method for the \f(CW\*(C`distanceUnit\*(C'\fR association.
.Sp
Input parameters: none
.Sp
Return value: the current value of the \f(CW\*(C`distanceUnit\*(C'\fR association : an instance of type \f(CW\*(C`Bio::MAGE::Measurement::DistanceUnit\*(C'\fR.
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if any input parameters are specified
.RE
.RS 4
.RE
.IP "security" 4
.IX Item "security"
Methods for the \f(CW\*(C`security\*(C'\fR association.
.Sp
From the MAGE-OM documentation:
.Sp
Information on the security for the instance of the class.
.RS 4
.ie n .IP "$val = $fiducial\->setSecurity($val)" 4
.el .IP "\f(CW$val\fR = \f(CW$fiducial\fR\->setSecurity($val)" 4
.IX Item "$val = $fiducial->setSecurity($val)"
The restricted setter method for the \f(CW\*(C`security\*(C'\fR association.
.Sp
Input parameters: the value to which the \f(CW\*(C`security\*(C'\fR association will be set : one of the accepted enumerated values.
.Sp
Return value: the current value of the \f(CW\*(C`security\*(C'\fR association : one of the accepted enumerated values.
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or
if too many input parameters are specified, or if \f(CW$val\fR is not an instance of class \f(CW\*(C`Bio::MAGE::AuditAndSecurity::Security\*(C'\fR
.ie n .IP "$val = $fiducial\->\fIgetSecurity()\fR" 4
.el .IP "\f(CW$val\fR = \f(CW$fiducial\fR\->\fIgetSecurity()\fR" 4
.IX Item "$val = $fiducial->getSecurity()"
The restricted getter method for the \f(CW\*(C`security\*(C'\fR association.
.Sp
Input parameters: none
.Sp
Return value: the current value of the \f(CW\*(C`security\*(C'\fR association : an instance of type \f(CW\*(C`Bio::MAGE::AuditAndSecurity::Security\*(C'\fR.
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if any input parameters are specified
.RE
.RS 4
.RE
.IP "fiducialType" 4
.IX Item "fiducialType"
Methods for the \f(CW\*(C`fiducialType\*(C'\fR association.
.Sp
From the MAGE-OM documentation:
.Sp
A descriptive string that indicates the type of a fiducial (e.g. the chrome border on an Affymetrix array, a laser ablation mark).
.RS 4
.ie n .IP "$val = $fiducial\->setFiducialType($val)" 4
.el .IP "\f(CW$val\fR = \f(CW$fiducial\fR\->setFiducialType($val)" 4
.IX Item "$val = $fiducial->setFiducialType($val)"
The restricted setter method for the \f(CW\*(C`fiducialType\*(C'\fR association.
.Sp
Input parameters: the value to which the \f(CW\*(C`fiducialType\*(C'\fR association will be set : one of the accepted enumerated values.
.Sp
Return value: the current value of the \f(CW\*(C`fiducialType\*(C'\fR association : one of the accepted enumerated values.
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or
if too many input parameters are specified, or if \f(CW$val\fR is not an instance of class \f(CW\*(C`Bio::MAGE::Description::OntologyEntry\*(C'\fR
.ie n .IP "$val = $fiducial\->\fIgetFiducialType()\fR" 4
.el .IP "\f(CW$val\fR = \f(CW$fiducial\fR\->\fIgetFiducialType()\fR" 4
.IX Item "$val = $fiducial->getFiducialType()"
The restricted getter method for the \f(CW\*(C`fiducialType\*(C'\fR association.
.Sp
Input parameters: none
.Sp
Return value: the current value of the \f(CW\*(C`fiducialType\*(C'\fR association : an instance of type \f(CW\*(C`Bio::MAGE::Description::OntologyEntry\*(C'\fR.
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if any input parameters are specified
.RE
.RS 4
.Sp
sub initialize {
.Sp
.Vb 2
\&  my $self = shift;
\&  return 1;
.Ve
.Sp
}
.RE
.SH "SLOTS, ATTRIBUTES, AND ASSOCIATIONS"
.IX Header "SLOTS, ATTRIBUTES, AND ASSOCIATIONS"
In the Perl implementation of MAGE-OM classes, there are
three types of class data members: \f(CW\*(C`slots\*(C'\fR, \f(CW\*(C`attributes\*(C'\fR, and
\&\f(CW\*(C`associations\*(C'\fR.
.SS "\s-1SLOTS\s0"
.IX Subsection "SLOTS"
This \s-1API\s0 uses the term \f(CW\*(C`slot\*(C'\fR to indicate a data member of the class
that was not present in the \s-1UML\s0 model and is used for mainly internal
purposes \- use only if you understand the inner workings of the
\&\s-1API.\s0 Most often slots are used by generic methods such as those in the
\&\s-1XML\s0 writing and reading classes.
.PP
Slots are implemented using unified getter/setter methods:
.ie n .IP "$var = $obj\->\fIslot_name()\fR;" 4
.el .IP "\f(CW$var\fR = \f(CW$obj\fR\->\fIslot_name()\fR;" 4
.IX Item "$var = $obj->slot_name();"
Retrieves the current value of the slot.
.ie n .IP "$new_var = $obj\->slot_name($new_var);" 4
.el .IP "\f(CW$new_var\fR = \f(CW$obj\fR\->slot_name($new_var);" 4
.IX Item "$new_var = $obj->slot_name($new_var);"
Store \f(CW$new_var\fR in the slot \- the return value is also \f(CW$new_var\fR.
.ie n .IP "@names = $obj\->\fIget_slot_names()\fR" 4
.el .IP "\f(CW@names\fR = \f(CW$obj\fR\->\fIget_slot_names()\fR" 4
.IX Item "@names = $obj->get_slot_names()"
Returns the list of all slots in the class.
.PP
\&\fB\s-1DATA CHECKING\s0\fR: No data type checking is made for these methods.
.SS "\s-1ATTRIBUTES AND ASSOCIATIONS\s0"
.IX Subsection "ATTRIBUTES AND ASSOCIATIONS"
The terms \f(CW\*(C`attribute\*(C'\fR and \f(CW\*(C`association\*(C'\fR indicate data members of the
class that were specified directly from the \s-1UML\s0 model.
.PP
In the Perl implementation of MAGE-OM classes,
association and attribute accessors are implemented using three
separate methods:
.IP "get*" 4
.IX Item "get*"
Retrieves the current value.
.Sp
\&\fB\s-1NOTE\s0\fR: For associations, if the association has list cardinality, an
array reference is returned.
.Sp
\&\fB\s-1DATA CHECKING\s0\fR: Ensure that no argument is provided.
.IP "set*" 4
.IX Item "set*"
Sets the current value, \fBreplacing\fR any existing value.
.Sp
\&\fB\s-1NOTE\s0\fR: For associations, if the association has list cardinality,
the argument must be an array reference. Because of this, you probably
should be using the add* methods.
.Sp
\&\fB\s-1DATA CHECKING\s0\fR: For attributes, ensure that a single value is
provided as the argument. For associations, if the association has
list cardinality, ensure that the argument is a reference to an array
of instances of the correct MAGE-OM class, otherwise
ensure that there is a single argument of the correct MAGE-OM class.
.IP "add*" 4
.IX Item "add*"
\&\fB\s-1NOTE\s0\fR: Only present in associations with list cardinality.
.Sp
Appends a list of objects to any values that may already be stored
in the association.
.Sp
\&\fB\s-1DATA CHECKING\s0\fR: Ensure that all arguments are of the correct MAGE-OM class.
.SS "\s-1GENERIC METHODS\s0"
.IX Subsection "GENERIC METHODS"
The unified base class of all MAGE-OM classes, \f(CW\*(C`Bio::MAGE::Base\*(C'\fR, provides a set of generic methods that
will operate on slots, attributes, and associations:
.ie n .IP "$val = $obj\->get_slot($name)" 4
.el .IP "\f(CW$val\fR = \f(CW$obj\fR\->get_slot($name)" 4
.IX Item "$val = $obj->get_slot($name)"
.PD 0
.ie n .IP "\e@list_ref = $obj\->get_slots(@name_list);" 4
.el .IP "\e@list_ref = \f(CW$obj\fR\->get_slots(@name_list);" 4
.IX Item "@list_ref = $obj->get_slots(@name_list);"
.ie n .IP "$val = $obj\->set_slot($name,$val)" 4
.el .IP "\f(CW$val\fR = \f(CW$obj\fR\->set_slot($name,$val)" 4
.IX Item "$val = $obj->set_slot($name,$val)"
.ie n .IP "$obj\->set_slots(%parameters)" 4
.el .IP "\f(CW$obj\fR\->set_slots(%parameters)" 4
.IX Item "$obj->set_slots(%parameters)"
.ie n .IP "$obj\->set_slots(\e@name_list, \e@value_list)" 4
.el .IP "\f(CW$obj\fR\->set_slots(\e@name_list, \e@value_list)" 4
.IX Item "$obj->set_slots(@name_list, @value_list)"
.PD
See elsewhere in this page for a detailed description of these
methods.
.SH "BUGS"
.IX Header "BUGS"
Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net)
.SH "AUTHOR"
.IX Header "AUTHOR"
Jason E. Stewart (jasons 'at' cpan 'dot' org)
.SH "SEE ALSO"
.IX Header "SEE ALSO"
\&\fIperl\fR\|(1).
.SH "POD ERRORS"
.IX Header "POD ERRORS"
Hey! \fBThe above document had some coding errors, which are explained below:\fR
.IP "Around line 395:" 4
.IX Item "Around line 395:"
\&'=item' outside of any '=over'
.IP "Around line 480:" 4
.IX Item "Around line 480:"
You forgot a '=back' before '=head2'
.IP "Around line 508:" 4
.IX Item "Around line 508:"
Expected '=item 2'
.IP "Around line 513:" 4
.IX Item "Around line 513:"
Expected '=item 3'
.IP "Around line 518:" 4
.IX Item "Around line 518:"
Expected '=item 4'